Genome projects have shown that metazoans generate a hugely diverse proteome from a limited number of genes. This finding underscores the importance of alternative splicing, through which a single gene can generate multiple structurally and functionally distinct protein isoforms. Moreover, recent transcriptome analyses with splicing-sensitive microarrays or deep sequencers have revealed that alternative splicing occurs in more than 90% of multi-exon genes in human (NPL 1) and over 60% of these cases are regulated in a tissue- and cell type-specific manner (NPL 2). Alternative splicing is regulated by auxiliary cis-elements with regulatory proteins that enhance or repress splicing of adjacent exons (NPL 3, 4) however, the mechanism by which a number of genes are regulated in various tissue-specific manner by a limited number of regulatory factors remains unclear.
In mammals, fibroblast growth factor-receptor 2 (FGFR2) is one of the best characterized gene in which mutually exclusive alternative splicing produces two isoforms. Exon 8 (also termed IIIb) isoform is specifically expressed in epithelial tissues, whereas exon 9 (or IIIc) isoform is selected in non-epithelial or mesenchymal tissues (NPL 5, 6). The structural difference between two splice isoforms markedly affects the specificity of ligand-receptor binding (NPL 7, 8, 9), and exon switching is shown to be essential for development in the mouse (NPL 10, 11). Several factors have been identified which positively or negatively regulate either of alternative exons of FGFR2 independently. For exon 8 regulation, Del Gatto-Konczak et al. found that heterogeneous nuclear ribonucleoprotein, hnRNP A1, binds to exon 8 (also termed K-SAM exon) as ESS (exonic splicing silencer) and represses its inclusion (NPL 12). Carstens et al. found the polypyrimidine tract binding protein (PTB) represses exon 8 inclusion through ISS-1 and ISS-2 (intronic splicing silencers-1 and 2) (NPL 13). Warzecha et al. recently cloned RBM35a and RBM35b as epithelia-specific activators of exon 8 inclusion, and renamed them epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESPR2), respectively (NPL 14). For exon 9 regualtion, Chen et al. found that Tra2beta represses the selection of exon 9 (NPL 15). Baraniak et al. reported that Fox2 represses selection of exon 9 through binding to a UGCAUG sequence in intron 8 (NPL 16). Hovhannisyan et al. found that a hnRNP M binds to ISS-3 and represses inclusion of exon 9 (NPL 17). Mauger et al. showed that hnRNP H and F interact with Fox2 and repress exon 9 inclusion (NPL 18). Also, presence of unknown enhancer is speculated for exon 9 inclusion through ISE (intronic splicing enhancer) in intron 9 (NPL 14).